2012 june 28 : jflat on centroid
@jflat06> i really want to get centroid mode in the game... 02:16:59 centroid mode? 02:18:22 <@jflat06> centroid mode makes things a lot faster at the cost of precision 02:18:34 <@jflat06> makes early-game much more managable 02:18:50 sounds nice :) 02:19:06 I might have considered submitting that as a request before... 02:19:07 just what we need 02:19:18 ...but didn't because I thought that this would be too much insider information 02:19:41 <@jflat06> the new alignment panel uses it 02:19:43 <@jflat06> in dev-prev 02:19:56 <@jflat06> the 'score' in the title bar calculates using centroid mode 02:20:22 <@jflat06> which basically means it treats sidechains as a single large 'atom' in a single position 02:20:28 jflat, centroid mode won't have the hiding contribution will it? 02:20:28 <@MikeCassidyToo> new dev to dl?? 02:20:49 <@jflat06> as of yesterday, yeah mike 02:20:49 Brow42: I doubt it 02:20:50 oh, it will? I knows sidechain orienation? 02:21:01 <@MikeCassidyToo> I got that one 02:21:10 <@jflat06> there was another new one today 02:21:14 <@jflat06> that resolves some autosave issues 02:21:20 After all, what centroid mode does is simplifying the side chain to one giant sphere 02:21:27 <@jflat06> yeah 02:21:27 So an entirely different score function has to be used 02:21:28 <@jflat06> basically 02:21:49 well, I just want it to know if I have the oranges and blues on the right side of the sheet 02:22:00 The side chain terms would have to be replaed with a lumped term that captures van der waals interactions, I think 02:22:02 <@jflat06> it approximates each AA sidechain by a single large atom 02:22:05 <@jflat06> so you never have to shake 02:22:14 that explains why it is call centroid mode 02:22:19 <@jflat06> yep 02:22:19 <@jflat06> lol 02:22:29 <@jflat06> but yeah, you have to use a different score function 02:22:31 I thought it replaced SEGMENTS with a large atom 02:22:32 Obviously that's a huge loss of information for long side chains 02:22:34 <@jflat06> or the game will crash... 02:22:35 E.g. Lysine 02:22:47 <@jflat06> not segments 02:22:51 <@jflat06> the backbone atoms are all there 02:22:54 <@jflat06> just the sidechain atoms 02:23:11 cool, this sounds like a good improvement for early game as you said 02:23:28 yeah, or arginine 02:24:11 <@jflat06> generally when someone uses rosetta on an extended chain, they'll use centroid mode, and then refine it later in fullatom mode 02:24:18 well, it will be interesting to see if centroid mode works in practice 02:24:27 <@jflat06> it works for the baker lab 02:24:28 <@jflat06> lol 02:24:57 <@jflat06> and i believe local minimize and the pull tool actually convert portions of the protein to centroid 02:25:03 <@jflat06> err local wiggle 02:25:20 How does that work? 02:26:12 <@jflat06> it just changes the residues in the copy of the protein it's working on temporarily while it's working, then copies the backbone atoms back when its done 02:26:14 <@jflat06> i think 02:26:41 <@jflat06> but yeah, it's pretty cool with the alignment tool 02:26:49 <@jflat06> you can immediately see the feedback of say, flipping a sheet 02:27:06 <@jflat06> if you shift by one, it gets horrible, and shifting another time will bump it right back up 02:32:36 jflat: I always like to try a new feature, so please let us try this new mode out, and we can give feedback on how it works 02:32:56 <@jflat06> if it was that simple, i would have done it long ago 02:33:06 <@jflat06> there's quite a bit of work that needs to be done to get it working in foldit 02:33:32 <@jflat06> the entire game assumes you have a full-atom pose everywhere 02:33:43 <@jflat06> it wouldn't take kindly to plugging a centroid pose in instead 02:33:44 <@jflat06> lol 02:34:35 How does centroid mode handle clashing/steric hindrance? 02:35:31 <@jflat06> clashing is all the same, dont know about the hindrance. 02:36:45 sounds like it's just one big ball 02:36:55 <@jflat06> yeah 02:37:03 <@jflat06> from my understanding 02:37:08 <@jflat06> seems dead useful though 02:37:09 so it won't pack right 02:37:24 *correctly 02:37:25 <@jflat06> well, it will pack 'approximately' 02:37:32 <@jflat06> but running repack on it will do nothing 02:37:33 <@jflat06> lol 02:37:37 <@jflat06> (aka shake) 02:37:49 <@jflat06> which is the reason why shaking does nothing to the score in the alignment panel 02:38:14 so the size of the ball depends on the size of the sidechain? That would sort of explain how it would avoid clashes. 02:38:16 Is the centroid score calculated the same way as well? 02:38:30 Namely, Foldit score = 8000 - (Energy score) * 10? 02:39:01 <@jflat06> @tokens, yeah. but you still get clashes if the atoms are too close 02:39:12 <@jflat06> and yes, it's the same function 02:39:22 <@jflat06> though with different score terms in the underlying energy function Category:Chat